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Nearly 14% of disease-causing germline variants result from disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing end up classified as variants of uncertain significance (VUS). We developed and validated an analytic workflow — Splice Effect Event Resolver (SPEER) — that uses mRNA sequencing to reveal significant deviations in splicing, pinpoints the DNA variants potentially responsible, and measures the deleterious effect of the altered splicing on mRNA transcripts, providing evidence to assess the pathogenicity of the variant. SPEER was used to analyze leukocyte RNA encoding 63 hereditary cancer syndrome genes in 20,317 individuals undergoing clinical genetic testing. Among 3,563 (17.5%) individuals with at least one DNA variant predicted to affect splicing, 971 (4.8%) had altered splicing with a deleterious effect on the transcript and 31 had altered splicing due to a DNA variant located outside our laboratory’s reportable range. Integrating SPEER results into variant interpretation allowed reclassification of VUS to P/LP in 0.4% and to B/LB in 5.9% of the 20,317 patients. SPEER evidence had a significantly higher impact on allowing P/LP and B/LB interpretations in non-White individuals than in non-Hispanic White individuals, illustrating that evidence derived from RNA splicing analysis may reduce ethnic/ancestral disparities in genetic testing.

Association results between minor alleles of 467 variants incorportated in cross tissue gene expression prediction model for the gene of CRHR1.

Supplementary Table 2. Results of the statistical analyses in BRCA mutation carriers.

Supplementary Table 1. The 3,248 SNPs included in the study

Online Supplementary Documents

Supplementary Table 3. Results of the statistical analyses of SNPs from project 12 in BRCA-mutation carriers affected or non-affected with breast cancer and according to their estrogen receptor status.

Large-scale genome-wide association studies (GWAS) have identified approximately 35 loci associated with epithelial ovarian cancer (EOC) risk. The majority of GWAS-identified disease susceptibility variants are located in noncoding regions, and causal genes underlying these associations remain largely unknown. Here, we performed a transcriptome-wide association study to search for novel genetic loci and plausible causal genes at known GWAS loci. We used RNA sequencing data (68 normal ovarian tissue samples from 68 individuals and 6,124 cross-tissue samples from 369 individuals) and high-density genotyping data from European descendants of the Genotype-Tissue Expression (GTEx V6) project to build ovarian and cross-tissue models of genetically regulated expression using elastic net methods. We evaluated 17,121 genes for their cis-predicted gene expression in relation to EOC risk using summary statistics data from GWAS of 97,898 women, including 29,396 EOC cases. With a Bonferroni-corrected significance level of P < 2.2 × 10−6, we identified 35 genes, including FZD4 at 11q14.2 (Z = 5.08, P = 3.83 × 10−7, the cross-tissue model; 1 Mb away from any GWAS-identified EOC risk variant), a potential novel locus for EOC risk. All other 34 significantly associated genes were located within 1 Mb of known GWAS-identified loci, including 23 genes at 6 loci not previously linked to EOC risk. Upon conditioning on nearby known EOC GWAS-identified variants, the associations for 31 genes disappeared and three genes remained (P < 1.47 × 10−3). These data identify one novel locus (FZD4) and 34 genes at 13 known EOC risk loci associated with EOC risk, providing new insights into EOC carcinogenesis.Significance: Transcriptomic analysis of a large cohort confirms earlier GWAS loci and reveals FZD4 as a novel locus associated with EOC risk. Cancer Res; 78(18); 5419–30. ©2018 AACR.

Background:BRCA1 and BRCA2 mutation carriers are at substantially increased risk for developing breast and ovarian cancer. The incomplete penetrance coupled with the variable age at diagnosis in carriers of the same mutation suggests the existence of genetic and nongenetic modifying factors. In this study, we evaluated the putative role of variants in many candidate modifier genes.Methods: Genotyping data from 15,252 BRCA1 and 8,211 BRCA2 mutation carriers, for known variants (n = 3,248) located within or around 445 candidate genes, were available through the iCOGS custom-designed array. Breast and ovarian cancer association analysis was performed within a retrospective cohort approach.Results: The observed P values of association ranged between 0.005 and 1.000. None of the variants was significantly associated with breast or ovarian cancer risk in either BRCA1 or BRCA2 mutation carriers, after multiple testing adjustments.Conclusion: There is little evidence that any of the evaluated candidate variants act as modifiers of breast and/or ovarian cancer risk in BRCA1 or BRCA2 mutation carriers.Impact: Genome-wide association studies have been more successful at identifying genetic modifiers of BRCA1/2 penetrance than candidate gene studies. Cancer Epidemiol Biomarkers Prev; 24(1); 308–16. ©2014 AACR.

Background & Aims Hereditary factors play a role in the development of colorectal cancer (CRC). Identification of germline predisposition can have implications on treatment and cancer prevention. This study aimed to determine the prevalence of pathogenic germline variants (PGVs) in CRC patients using a universal testing approach, association with clinical outcomes, and the uptake of family variant testing. Methods We performed a prospective multisite study of germline sequencing using a more than 80-gene next-generation sequencing platform among CRC patients (not selected for age or family history) receiving care at Mayo Clinic Cancer Centers between April 1, 2018, and March 31, 2020. Results Of 361 patients, the median age was 57 years (SD, 12.4 y), 43.5% were female, 82% were white, and 38.2% had stage IV disease. PGVs were found in 15.5% (n = 56) of patients, including 44 in moderate- and high-penetrance cancer susceptibility genes. Thirty-four (9.4%) patients had incremental clinically actionable findings that would not have been detected by practice guideline criteria or a CRC-specific gene panel. Only younger age at diagnosis was associated with the presence of PGVs (odds ratio, 1.99; 95% CI, 1.12–3.56). After a median follow-up period of 20.7 months, no differences in overall survival were seen between those with or without a PGV (P = .2). Eleven percent of patients had modifications in their treatment based on genetic findings. Family cascade testing was low (16%). Conclusions Universal multigene panel testing in CRC was associated with a modest, but significant, detection of heritable mutations over guideline-based testing. One in 10 patients had changes in their management based on test results. Uptake of cascade family testing was low, which is a concerning observation that warrants further study.

PURPOSE Strict clinical criteria used by Medicare for germline testing for Lynch syndrome (LS) could lead to missed diagnoses of hereditary cancer syndromes given variable individual and family phenotypes. The aim of this study was to compare rates and spectrum of pathogenic or likely pathogenic (P/LP) variants in LS and other hereditary cancer genes on the basis of meeting Medicare LS testing criteria. METHODS Retrospective review of Medicare beneficiaries who had multigene panel testing with an indication of personal or family history of colorectal cancer (CRC) was performed. Ordering providers determined if Medicare LS criteria were met. The results of genetic testing were compared on the basis of whether or not Medicare testing criteria were met. RESULTS Among 639 Medicare beneficiaries, 495 (77.5%) met testing criteria. Overall rates of P/LP variant identification were similar between those meeting and not meeting testing criteria (18.4% v 11.8%; P = .06). LS was diagnosed more frequently among those meeting testing criteria (10.1% v 4.9%; P = .05). No statistical differences were found in rates of P/LP variant identification for non-LS CRC genes (5.3% v 5.6%; P = .89) or non-CRC genes (4.2% v 2.1%; P = .23). PMS2, MUTYH, and ATM P/LP variants were found at higher rates among those outside of criteria. CONCLUSION Among Medicare beneficiaries undergoing genetic testing for suspected LS, rates of P/LP variants in actionable cancer genes were similar regardless of whether testing criteria were met. Current testing criteria fail to identify individuals with P/LP variants in PMS2 and other actionable cancer genes. Relaxing LS testing criteria could improve identification of individuals with hereditary cancer syndromes among Medicare beneficiaries.

PurposeTo evaluate the impact of technically challenging variants on the implementation, validation, and diagnostic yield of commonly used clinical genetic tests. Such variants include large indels, small CNVs, complex alterations, and variants in low-complexity or segmentally duplicated regions.MethodsAn interlaboratory pilot study used novel synthetic specimens to assess detection of challenging variant types by various NGS-based workflows. One well-performing workflow was further validated and used in clinician-ordered testing of more than 450,000 patients.ResultsIn the interlaboratory study, only two of 13 challenging variants were detected by all 10 workflows, and just three workflows detected all 13. Limitations were also observed among 11 less-challenging indels. In clinical testing, 21.6% of patients carried one or more pathogenic variants, of which 13.8% (17,561) were classified as technically challenging. These variants were of diverse types, affecting 556 of 1,217 genes across hereditary cancer, cardiovascular, neurological, pediatric, reproductive carrier screening, and other indicated tests.ConclusionThe analytic and clinical sensitivity of NGS workflows can vary considerably, particularly for prevalent, technically challenging variants. This can have important implications for the design and validation of tests (by laboratories) and the selection of tests (by clinicians) for a wide range of clinical indications.

ImportanceIn 2020, some health insurance plans updated their medical policy to cover germline genetic testing for all patients diagnosed with colorectal cancer (CRC). Guidelines for universal tumor screening via microsatellite instability and/or immunohistochemistry (MSI/IHC) for mismatch repair protein expression for patients with CRC have been in place since 2009.ObjectivesTo examine whether uptake of MSI/IHC screening and germline genetic testing in patients with CRC has improved under these policies and to identify actionable findings and management implications for patients referred for germline genetic testing.Design, Setting, and ParticipantsThe multicenter, retrospective cohort study comprised 2 analyses of patients 18 years or older who were diagnosed with CRC between January 1, 2017, and December 31, 2020. The first analysis used an insurance claims data set to examine use of MSI/IHC screening and germline genetic testing for patients diagnosed with CRC between 2017 and 2020 and treated with systemic therapy. The second comprised patients with CRC who had germline genetic testing performed in 2020 that was billed under a universal testing policy.Main Outcomes and MeasuresPatient demographic characteristics, clinical information, and use of MSI/IHC screening and germline genetic testing were analyzed.ResultsFor 9066 patients with newly diagnosed CRC (mean [SD] age, 64.2 [12.7] years; 4964 [54.8%] male), administrative claims data indicated that MSI/IHC was performed in 6645 eligible patients (73.3%) during the study period, with 2288 (25.2%) not receiving MSI/IHC despite being eligible for coverage. Analysis of a second cohort of 55 595 patients with CRC diagnosed in 2020 and covered by insurance found that only 1675 (3.0%) received germline genetic testing. In a subset of patients for whom germline genetic testing results were available, 1 in 6 patients had pathogenic or likely pathogenic variants, with most of these patients having variants with established clinical actionability.Conclusions and RelevanceThis nationwide cohort study found suboptimal rates of MSI/IHC screening and germline genetic testing uptake, resulting in clinically actionable genetic data being unavailable to patients diagnosed with CRC, despite universal eligibility. Effective strategies are required to address barriers to implementation of evidence-based universal testing policies that support precision treatment and optimal care management for patients with CRC.

Genetic testing can guide management of both cardiomyopathies and arrhythmias, but cost, yield, and uncertain results can be barriers to its use. It is unknown whether combined disease testing can improve diagnostic yield and clinical utility for patients with a suspected genetic cardiomyopathy or arrhythmia.To evaluate the diagnostic yield and clinical management implications of combined cardiomyopathy and arrhythmia genetic testing through a no-charge, sponsored program for patients with a suspected genetic cardiomyopathy or arrhythmia.This cohort study involved a retrospective review of DNA sequencing results for cardiomyopathy- and arrhythmia-associated genes. The study included 4782 patients with a suspected genetic cardiomyopathy or arrhythmia who were referred for genetic testing by 1203 clinicians; all patients participated in a no-charge, sponsored genetic testing program for cases of suspected genetic cardiomyopathy and arrhythmia at a single testing site from July 12, 2019, through July 9, 2020.Positive gene findings from combined cardiomyopathy and arrhythmia testing were compared with findings from smaller subtype-specific gene panels and clinician-provided diagnoses.Among 4782 patients (mean [SD] age, 40.5 [21.3] years; 2551 male [53.3%]) who received genetic testing, 39 patients (0.8%) were Ashkenazi Jewish, 113 (2.4%) were Asian, 571 (11.9%) were Black or African American, 375 (7.8%) were Hispanic, 2866 (59.9%) were White, 240 (5.0%) were of multiple races and/or ethnicities, 138 (2.9%) were of other races and/or ethnicities, and 440 (9.2%) were of unknown race and/or ethnicity. A positive result (molecular diagnosis) was confirmed in 954 of 4782 patients (19.9%). Of those, 630 patients with positive results (66.0%) had the potential to inform clinical management associated with adverse clinical outcomes, increased arrhythmia risk, or targeted therapies. Combined cardiomyopathy and arrhythmia gene panel testing identified clinically relevant variants for 1 in 5 patients suspected of having a genetic cardiomyopathy or arrhythmia. If only patients with a high suspicion of genetic cardiomyopathy or arrhythmia had been tested, at least 137 positive results (14.4%) would have been missed. If testing had been restricted to panels associated with the clinician-provided diagnostic indications, 75 of 689 positive results (10.9%) would have been missed; 27 of 75 findings (36.0%) gained through combined testing involved a cardiomyopathy indication with an arrhythmia genetic finding or vice versa. Cascade testing of family members yielded 402 of 958 positive results (42.0%). Overall, 2446 of 4782 patients (51.2%) had only variants of uncertain significance. Patients referred for arrhythmogenic cardiomyopathy had the lowest rate of variants of uncertain significance (81 of 176 patients [46.0%]), and patients referred for catecholaminergic polymorphic ventricular tachycardia had the highest rate (48 of 76 patients [63.2%]).In this study, comprehensive genetic testing for cardiomyopathies and arrhythmias revealed diagnoses that would have been missed by disease-specific testing. In addition, comprehensive testing provided diagnostic and prognostic information that could have potentially changed management and monitoring strategies for patients and their family members. These results suggest that this improved diagnostic yield may outweigh the burden of uncertain results.

Summary Most rare clinical missense variants cannot currently be classified as pathogenic or benign. Deficiency in human 5,10-methylenetetrahydrofolate reductase (MTHFR), the most common inherited disorder of folate metabolism, is caused primarily by rare missense variants. Further complicating variant interpretation, variant impacts often depend on environment. An important example of this phenomenon is the MTHFR variant p.Ala222Val (c.665C>T), which is carried by half of all humans and has a phenotypic impact that depends on dietary folate. Here we describe the results of 98,336 variant functional-impact assays, covering nearly all possible MTHFR amino acid substitutions in four folinate environments, each in the presence and absence of p.Ala222Val. The resulting atlas of MTHFR variant effects reveals many complex dependencies on both folinate and p.Ala222Val. MTHFR atlas scores can distinguish pathogenic from benign variants and, among individuals with severe MTHFR deficiency, correlate with age of disease onset. Providing a powerful tool for understanding structure-function relationships, the atlas suggests a role for a disordered loop in retaining cofactor at the active site and identifies variants that enable escape of inhibition by S-adenosylmethionine. Thus, a model based on eight MTHFR variant effect maps illustrates how shifting landscapes of environment- and genetic-background-dependent missense variation can inform our clinical, structural, and functional understanding of MTHFR deficiency.

Background: Growing evidence indicates that restrictive criteria for determining eligibility of breast cancer patients for germline genetic testing (e.g. NCCN, etc.) can missa significant number who may benefit from testing. However, the clinical utility and outcomes of patients with germline pathogenic variants (“positive patients”) who fall outside of current criteria has not been studied,and there is limited data on the clinical impact of nonBRCA pathogenic variantsin patients who fall inside testing criteria. We present longitudinal data from a previous cohort of patients, who are being followed in a new genetics registry that correlates germlinetest results with impact on clinical decision making, disease status, treatmentcourse, clinical trial enrollment and overall survival. Methods: A large multi-center IRB approved prospective Registry initiated in 2017 collected andanalyzed data on 959 breast cancer patients, newly or previously diagnosed, atthe time of genetic test result return (Beitsch et al. JCO 2018)1.This abstract presents clinical data over the intervening 18-24 months on patients with positive variants (83) both in-criteria (IC) and out-of-criteria (OOC),collected via medical record review as part of the iGAP Registry(igapregistry.org), sponsored by Medneon (Cupertino, Ca). Results: Of the 44 positive patients for whom longitudinalclinical outcomes data have been analyzed to date, 24 met guidelines fortesting and 20 did not. 6 had a history of additional primary cancers at thetime of testing. 40/44 patients are disease free; of these 20 were IC,20 were OOC. 1/44 has stable disease and was OCC. 3/44 have progressive orrecurrent breast cancer and 2 were OCC and 1 was IC. 13/44received chemotherapy; 6 IC and 7 OOC. 5 patients (with mutations in BRCA1,BRCA2, PALB2, MUTYH) received carboplatin consistent with the sensitivity toplatinum agents conferred by deficiencies in homologous recombination (HR) andbase-excision repair (BER). Longitudinal outcomes stratified by gene result arein Table 1. Conclusions:This studyprovides initial evidence for the impact of germline genetic test results onlongitudinal patient outcomes, stratified by gene. It also begins to correlategermline results and chemotherapy, as 3/5 OOC patients receiving carboplatinhad mutations in HR or BER genes. This raises the possibility that certain treatment advantages and other beneficial changes in management could bewithheld from OOC patients if restrictive criteria persist, as well as limiting the opportunities for possible preventive interventions for their at-risk family members 1. BeitschPD, Whitworth PW, Hughes K, et al. Underdiagnosis of Hereditary Breast Cancer:Are Genetic Testing Guidelines a Tool or an Obstacle?. J Clin Oncol.2019;37(6):453-460. doi:10.1200/JCO.18.01631 Table 1Positive Gene Variant# reported mutations-by geneSubject Health Status Disease FreeSubject Health Status Stable or Progressive DiseaseNCCN # ICNCCN # OOCATM22002BLM11001BRCA122020BRCA255041CHEK266033DIS3L211001FH11010MITF11010MSH611001MUTYH98127NBN22011NF110101NTLH111001PALB232121RAD5011010RAD51C22011RAD51D32112RECQL422011VHL11010 Citation Format: Peter Beitsch, Rakesh Patel, Pat Whitworth, Barry Rosen, Rick Brown, Gia Compagnoni, Linsey Gold, Ian Grady, Edward Esplin, Sarah Nielsen, Max Brown, Melissa Trudrung, Chloe Wernecke, Mary Kay Hardwick, Robert Nussbaum. Longitudinal clinical outcomes of a multi-center universal genetic testing registry [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-30.

Background:Therapeutic and risk management options have expanded for patients harboring pathogenic variants (PVs) in cancer predisposition genes. Historically, testing costs and clinical implementation challenges led to restrictive testing guidelines in many countries. Increasing evidence demonstrates that narrow criteria will miss patients with potentially actionable PVs and broader testing is a cost-effective way to identify patients (and their family members) with PVs. Here we assess the efficacy of multiple international testing guidelines in identifying breast cancer patients with clinically actionable PVs. Methods:We reanalyzed a prospective cohort of breast cancer (BC) patients referred by their providers for multigene germline genetic testing (PMID: 30526229) 50% of which met U.S. testing criteria, by design. The is a cohort of U.S.-based patients, primarily Caucasian of Northern European ancestry. We applied testing guidelines from Australia, U.K. and 2 Canadian provinces (Ontario, British Columbia) to this cohort to determine their efficacy in selecting patients with PVs. These countries were chosen because of their single-payer healthcare model and their similar ethnic distribution to the U.S. Analysis focused on yield of PVs in high risk (>4x risk compared to general population) breast/ovarian (BC/OV) cancer genes. Results:Table 1 displays the distribution of in criteria (IC) vs. out of criteria (OOC) patients by country/testing criteria. Over 75% of patients in each country/province analyzed were OOC. Rates of PVs were similar between IC and OOC patients across countries. Existing Canadian, Australian and U.K. criteria missed up to 30% of patients with high risk PVs (Table 1). The majority (>80%) of PVs in OOC patients were in genes with published management guidelines. Conclusions:In our cohort, select ex-U.S. testing criteria identified Table 1. Findings in IC vs. OOC patientsOverallIn criteria Out of criteriaCountry/providenceGuidelineTotal n of cohortIC (% of total cohort)OOC (% of total cohort)Total PV IC (% of IC cohort)Total PV OOC (% of OOC cohort)High risk^ PVs (% of total PVs)High risk^ PVs (% of total PVs)U.S.NCCN953473 (49.6)480 (50.4)43 (9.1)40 (8.3)22 (26.5)8 (9.6)OntarioMOHLTC953210 (22.0)743 (78.0)18 (8.6)65 (8.7)5 (6.0)25 (30.1)B.C.BCHCP953203 (21.3)750 (78.7)24 (11.8)59 (7.9)9 (10.8)19 (22.9)AustraliaeviQ953180 (18.9)773 (81.1)19 (10.6)64 (8.3)12 (14.5)18 (21.7)U.K.NICE*826**127 (14.7)736 (85.3)11 (8.7)64 (8.7)6 (7.2)22 (26.5)US, United States; B.C., British Columbia; UK, United KingdomNCCN, National Comprehensive Cancer Network v. 2017MOHLTC, Ministry of Health and Long Term Care BCHCP, BC Provincial Health Services Authority Hereditary Cancer Program NICE, National Institute for Health Care Excellence*testing eligibility requires >10% BRCA mutation detection rate, typically assessed by BOADICEA model in the UK but for this cohort risk estimates were only available via BRCAPro ** BRCAPro scores were not available for the full cohort ^Includes BRCA1, BRCA2, PALB2, TP53, RAD51C, RAD51D, MSH6 Citation Format: Sarah M Nielsen, Peter Beitsch, Pat Whitworth, Emily Decker, Natalie Rickers, Hana Sroka, Alekhya Narravula, Ed D Esplin, Robert L. Nussbaum. Pathogenic variants in hereditary cancer syndrome genes are prevalent among breast cancer patients not meeting various ex-U.S. genetic testing guidelines [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-14.

Background: Hereditary factors play a key role in the risk of developing breast cancers. Identification of a germline predisposition can have important implications for treatment decisions, risk-reducing interventions, cancer screening, and testing for family members. Aim: To determine the prevalence of pathogenic or likely pathogenic germline mutations (P/LP) using a “universal” testing approach and uptake of no-cost cascade family testing in patients with breast cancer. Methods: We undertook a prospective multi-site study of germline genetic alterations among breast cancer patients receiving care at Mayo Clinic cancer centers in Rochester, MN; Eau Claire, WI; Jacksonville, FL and Phoenix, AZ between April 1, 2018 and March 31, 2020. Patients with a new or active breast cancer diagnosis (all stages) irrespective of cancer family history were tested with a >80-gene next generation sequencing panel.Results: Of 390 patients, the median age was 58 years (SD 12.3), 1% were male, 85% were white and 28% had advanced (stage 3-4) disease. P/LP were found in 12.1% (n=47) of patients, including 29 in moderate and high penetrance cancer susceptibility genes. 13 (3.3%) patients had mutations in BRCA1 or 2, while 33 (8.4%) had mutations in BRCAness (ATM, BAP1, BARD1, BLM, BRCA1, BRCA2, BRIP1, CHEK2, NBN, PALB2, RAD50, RAD51C, RAD51D, WRN) associated genes. Of the P/LP findings the most frequent aberrations were in BRCA2 (13.5%), BRCA1 (11.5%), CHEK2 (11.5%), MUTYH (11.5%), and WRN (9.6%). Variants of uncertain significance were found in 209 (53.6%) including 26 (6.6%) with concurrent P/LP and VUS. 37 (9.4%) patients had mutations associated with published management recommendations, precision therapies and/or clinical trial eligibility. 10 (2.6%) patients had P/LP that would not have met current screening guidelines, including 4 with moderate or high penetrance mutations. Patients with younger age of diagnosis were less likely than patients with older age of diagnosis to have a P/LP mutation (OR= 0.47, 95%CI: 0.25-0.90 p = 0.020). Only 10 (21%) patients with P/LP had family members undergo familial site- specific testing at no cost.Conclusions: In this prospective multi-center study of unselected breast cancer patients, universal multi-gene panel testing found that 1 in 8 patients harbor P/LP germline variants. Current guidelines were able to identify the majority of patients with P/LP mutations. Familial site specific testing is greatly under-utilized even when cost is not a barrier. Multigene panels impact cancer patient care by identifying precision medicine treatment interventions, and guiding long-term medical management and preventive surveillance. Citation Format: Brenda Ernst, Natalie Ertz-Archambault, Deborah J Rhodes, Donald W Northfelt, Myra Wick, Douglas L Riegert-Johnson, Scott Okuno, Katie Kunze, Michael Golafshar, Cindy M Azevedo, PLS Uson Junior, ED Esplin, Robert Nussbaum, Margaret Klint, Sarah Mantia, Megan Hager, Keith Stewart, Niloy Jewel Samadder. Universal genetic testing in breast cancer patients: A multi-center prospective study [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD10-05.

Motivation When rare missense variants are clinically interpreted as to their pathogenicity, most are classified as variants of uncertain significance (VUS). Although functional assays can provide strong evidence for variant classification, such results are generally unavailable. Multiplexed assays of variant effect can generate experimental ‘variant effect maps’ that score nearly all possible missense variants in selected protein targets for their impact on protein function. However, these efforts have not always prioritized proteins for which variant effect maps would have the greatest impact on clinical variant interpretation. Results Here, we mined databases of clinically interpreted variants and applied three strategies, each building on the previous, to prioritize genes for systematic functional testing of missense variation. The strategies ranked genes (i) by the number of unique missense VUS that had been reported to ClinVar; (ii) by movability- and reappearance-weighted impact scores, to give extra weight to reappearing, movable VUS and (iii) by difficulty-adjusted impact scores, to account for the more resource-intensive nature of generating variant effect maps for longer genes. Our results could be used to guide systematic functional testing of missense variation toward greater impact on clinical variant interpretation. Availability and implementation Source code available at: https://github.com/rothlab/mave-gene-prioritization Supplementary information Supplementary data are available at Bioinformatics online.

Consensus guidelines for hereditary breast and ovarian cancer include management recommendations for pathogenic/likely pathogenic (P/LP) variants in

Secondary genomic findings are increasingly being returned to individuals as opportunistic screening results. A secondary finding offers the chance to identify and mitigate disease that may otherwise be unrecognized in an individual. As a form of screening, secondary findings must be considered differently from sequencing results in a diagnostic setting. For these reasons, clinicians should employ an evaluation and long-term management strategy that accounts for both the increased disease risk associated with a secondary finding and the lower positive predictive value of a screening result compared to an indication-based testing result. Here we describe an approach to the clinical evaluation and management of an individual who presents with a secondary finding. This approach enumerates five domains of evaluation—(1) medical history, (2) physical exam, (3) family history, (4) diagnostic phenotypic testing, and (5) variant correlation—through which a clinician can distinguish a molecular finding from a clinicomolecular diagnosis of genomic disease. With this framework, both geneticists and non-geneticist clinicians can optimize their ability to detect and mitigate genomic disease while avoiding the pitfalls of overdiagnosis. Our goal with this approach is to help clinicians translate secondary findings into meaningful recognition, treatment, and prevention of disease.

Background: With the rise of precision medicine, hereditary cancer germline testing and tumor genetic testing have been increasingly used to inform the management of patients with cancer. Recent studies report that approximately 10% of patient’s tumors have clinically significant variants in genes known to predispose to a hereditary cancer syndrome. Here we report the concordance rate between tumor genetic testing and germline genetic testing in patients with breast cancer and review its impact on the patients’ management and implications for their relatives. Methods: In this study, we used de-identified data from 101 consecutive patients with breast cancer who underwent tumor genetic testing followed by germline testing with NGS-based hereditary cancer gene panels. Results: Tumor genetic testing results included likely pathogenic or pathogenic (LP/P) variants in BRCA2 (21%), BRCA1 (20%), TP53 (10%), CDH1 (7%), ATM (4.3%), PALB2,CHEK2, and PTEN (3.7% each), and PIK3CA (2.5%) among 22 other genes. In 33/101 cases (33%) the P/LP variant was also detected in the germline. Genes in which disease-causing variants were most frequently confirmed to be in the germline included: BRCA2 (36%), BRCA1(21%), PALB2 (12%), and CHEK2 (12%). Variants in ATM, FH, FANCA, and MSH6 were confirmed in the germline in Conclusions: A significant proportion (33%) of patients with clinically significant variants in tumors were identified to carry the same variant in the germline, uncovering a previously unknown risk of hereditary breast cancer disorder. Notably, some genes had a high probability of variants occurring in the germline, while others were primarily seen in tumors. Performing simultaneous germline and tumor testing may inform susceptibility to a hereditary cancer disorder, identify targets for precision therapy, early detection of secondary malignancies, and guide genetic counseling for relatives. Citation Format: Daniel E Pineda-Alvarez, Scott T Michalski, Meaghan Russell, Shan Yang, Ihn Young Song, Robert L Nussbaum, Edward D. Esplin. Breast cancer tumor sequencing coupled with germline genetic testing aids the identification of at-risk individuals for hereditary breast cancer disorders [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-09-08.

Background The slow delayed rectifier potassium current IKs is crucial for the repolarization of the cardiac action potential. It is conducted by the voltage-gated channel KV 7.1 encoded by KCNQ1, together with its β-subunit KCNE1. Loss-of-function (LOF) mutations in KCNQ1 have been associated with heritable cardiac arrhythmias such as Long QT syndrome (LQTS). This disease is characterized by prolonged ventricular repolarization and propensity to ventricular tachyarrhythmia that may lead to syncope, cardiac arrest, and sudden death. We aimed to functionally characterize two KV 7.1 mutations (p.A150T and p.L374H) identified in two independent LQTS patients with different severity of disease phenotype, family history, and co-segregation of LQTS. Methods We performed whole-cell patch clamp recordings in CHO-K1 cells, and confocal imaging in Madin-Darby Canine Kidney (MDCK) cells. Results IKs -A150T showed significantly decreased current amplitudes from above +20 mV (approximately 52% decrease at +40 mV), but demonstrated cell membrane localization similar to wild-type (WT). IKs -L374H, however, exhibited a complete LOF compared to WT channels. Confocal imaging showed endoplasmic reticulum retention of the channel in MDCK cells. Mimicking the heterozygous state of the patients by co-expressing WT and mutant subunits resulted in an approximately 22% decrease in current at +40 mV for A150T. The L374H mutation showed a more pronounced effect (62% reduction at +40 mV compared to WT channel). Conclusion Both mutations, KV 7.1 A150T and L374H, led to loss of channel function. The degree of LOF may mirror the disease phenotype observed in the patients.

Little is known about the true rate of pathogenic (P)/likely pathogenic (LP) germline alterations in Hispanic men with prostate cancer as most studies analyzing the prevalence of P/LP germline alterations were performed in a largely non-Hispanic white population (NHW).We performed a retrospective analysis of two separate cohorts of men with prostate cancer: (1) a multicenter cohort of 17,256 men who underwent germline testing in a CLIA-certified laboratory and (2) a single-center cohort of all men eligible for germline testing between 2018 and 2020. The proportions of P/LP alterations and variants of uncertain significance (VUS) were computed. Fisher's exact test was used to compare germline alteration rates for significance. A multivariate logistic regression was performed adjusting for demographic and clinical factors to examine factors associated with germline testing.In the multicenter cohort, the rate of P/LP germline alterations among self-reported Hispanic men was 7.1%, which was lower than self-reported NHW men (9.7% vs. 7.1%, p = 0.058), but was not statistically significant. The VUS rate was significantly higher among the Hispanic cohort (21.5% vs. 16.6%, p = 0.005). In the single-center cohort, 136 Hispanic patients were eligible for testing of which 34 underwent germline testing (26.1%, N = 34/136). Of all prostate cancer patients in the single-center cohort undergoing germline testing (n = 173), the rate of P/LP alterations in Hispanic patients was not significantly different compared to NHW patients (14.7% vs. 12.2%, p = 0.77). The rate of VUS in Hispanic patients was significantly higher than that of NHW patients (20.6% vs. 7.2%, p = 0.047).The P/LP germline alteration rate in our cohorts was similar between Hispanic and NHW men. The rate of VUS was significantly higher in Hispanic men, a consequence of undertesting in minority populations. These data support that Hispanic men with prostate cancer should be screened for germline testing similar to NHW men.

BACKGROUND: Inherited germline TP53 pathogenic and likely pathogenic mutations (gTP53) cause autosomal dominant multicancer predisposition including Li-Fraumeni syndrome (LFS). However, there is no known association of prostate cancer with gTP53. OBJECTIVE: To determine whether gTP53 predisposes to prostate cancer. DESIGN, SETTING, AND PARTICIPANTS: This multi-institutional retrospective study characterizes prostate cancer incidence in a cohort of LFS males and gTP53 prevalence in a prostate cancer cohort. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: We evaluated the spectrum of gTP53 variants and clinical features associated with prostate cancer. RESULTS AND LIMITATIONS: We identified 31 prostate cancer cases among 163 adult LFS males, including 26 of 54 aged ≥50 yr. Among 117 LFS males without prostate cancer at the time of genetic testing, six were diagnosed with prostate cancer over a median (interquartile range [IQR]) of 3.0 (1.3–7.2) yr of follow-up, a 25-fold increased risk (95% confidence interval [CI] 9.2–55; p < 0.0001). We identified gTP53 in 38 of 6850 males (0.6%) in the prostate cancer cohort, a relative risk 9.1-fold higher than that of population controls (95% CI 6.2–14; p < 0.0001; gnomAD). We observed hotspots at the sites of attenuated mutations not associated with classic LFS. Two-thirds of available gTP53 prostate tumors had somatic inactivation of the second TP53 allele. Among gTP53 prostate cancer cases in this study, the median age at diagnosis was 56 (IQR: 51–62) yr, 42% had Gleason ≥8 tumors, and 30% had advanced disease at diagnosis. CONCLUSIONS: Complementary analyses of prostate cancer incidence in LFS males and gTP53 prevalence in prostate cancer cohorts suggest that gTP53 predisposes to aggressive prostate cancer. Prostate cancer should be considered as part of LFS screening protocols and TP53 considered in germline prostate cancer susceptibility testing. PATIENT SUMMARY: Inherited mutations in the TP53 gene are likely to predispose men to aggressive prostate cancer.

Introduction: Professional guidelines support genetic testing (GT) for dilated, hypertrophic, restrictive, arrhythmogenic, and peripartum cardiomyopathy to confirm a diagnosis, guide management, enable clinical trials, and/or allow more informed genetic counseling. Analysis of de-identified data from a commercial laboratory showed that 1 in 4 individuals who had cardiomyopathy GT billed to a national health insurer had a positive result; however, which patients undergo GT is largely unknown. Hypothesis: GT is underutilized in patients with genetic cardiomyopathy. Methods: A retrospective analysis was conducted using commercial and Medicare claims data from the UnitedHealth Group Clinical Discovery Database. The GT-cohort (index: GT dates 1/1/2017-12/31/2020) included patients with 12-months pre-index data including ≥1 ICD-10 codes associated with genetic or unspecified cardiomyopathy and GT Current Procedural Terminology (CPT) code(s). The non-GT cohort (index: outpatient visit dates 1/1/2017-12/31/2020 with 12-month pre-index data) had the same ICD codes, but no GT CPT code. Individuals with a personal and/or family history of cancer were excluded to avoid patients who had GT for cancer. Multivariable logistic regression analysis was performed to examine factors associated with GT. Results: Of 300,127 patients with cardiomyopathy, 3,287 (1.1%) had a GT CPT code. Factors that predicted a higher likelihood of GT (p < 0.05) included being younger, living in an area with a higher education level, commercial insurance, no diagnosis of diabetes or myocardial infarction, diagnosis of mild liver disease, a higher number of outpatient medical and cardiology visits, cardiac-related hospitalizations (shorter length-of-stay), a higher number of 30-day all-cause readmissions, a higher number of cardiomyopathy diagnoses, and except for peripartum, all genetic cardiomyopathy types. Conclusions: Only 1.1% of patients with a cardiomyopathy ICD code had a GT claim. Considering a potential 25% testing yield, a larger portion could have benefited from a genetics guided diagnosis. More research is needed to investigate barriers related to GT and improve our ability to identify those who could benefit from cardiomyopathy genetic testing.

INTRODUCTION AND OBJECTIVE:Pathogenic/likely pathogenic (P/LP) germline genetic variants occur in ∼10-15% of all prostate cancer (PCa) patients. However, complicated and restrictive testing guideli...

Background The use of proactive genetic screening for disease prevention and early detection is not yet widespread. Professional practice guidelines from the American College of Medical Genetics and Genomics (ACMG) have encouraged reporting pathogenic variants that confer personal risk for actionable monogenic hereditary disorders, but only as secondary findings from exome or genome sequencing. The Centers for Disease Control and Prevention (CDC) recognizes the potential public health impact of three Tier 1 actionable disorders. Here, we report results of a large multi-center cohort study to determine the yield and potential value of screening healthy individuals for variants associated with a broad range of actionable monogenic disorders, outside the context of secondary findings. Methods Eligible adults were offered a proactive genetic screening test by health care providers in a variety of clinical settings. The screening panel based on next-generation sequencing contained up to 147 genes associated with monogenic disorders within cancer, cardiovascular, and other important clinical areas. Sequence and intragenic copy number variants classified as pathogenic, likely pathogenic, pathogenic (low penetrance), or increased risk allele were considered clinically significant and reported. Results were analyzed by clinical area and severity/burden of disease using chi-square tests without Yates’ correction. Results Among 10,478 unrelated adults screened, 1619 (15.5%) had results indicating personal risk for an actionable monogenic disorder. In contrast, only 3.1 to 5.2% had clinically reportable variants in genes suggested by the ACMG version 2 secondary findings list to be examined during exome or genome sequencing, and 2% had reportable variants related to CDC Tier 1 conditions. Among patients, 649 (6.2%) were positive for a genotype associated with a disease of high severity/burden, including hereditary cancer syndromes, cardiovascular disorders, or malignant hyperthermia susceptibility. Conclusions This is one of the first real-world examples of specialists and primary care providers using genetic screening with a multi-gene panel to identify health risks in their patients. Nearly one in six individuals screened for variants associated with actionable monogenic disorders had clinically significant results. These findings provide a foundation for further studies to assess the role of genetic screening as part of regular medical care.

Background Pathogenic variation in the ATP1A3 ‐encoded sodium‐potassium ATPase, ATP1A3, is responsible for alternating hemiplegia of childhood (AHC). Although these patients experience a high rate of sudden unexpected death in epilepsy, the pathophysiologic basis for this risk remains unknown. The objective was to determine the role of ATP1A3 genetic variants on cardiac outcomes as determined by QT and corrected QT (QTc) measurements. Methods and Results We analyzed 12‐lead ECG recordings from 62 patients (male subjects=31, female subjects=31) referred for AHC evaluation. Patients were grouped according to AHC presentation (typical versus atypical), ATP1A3 variant status (positive versus negative), and ATP1A3 variant (D801N versus other variants). Manual remeasurements of QT intervals and QTc calculations were performed by 2 pediatric electrophysiologists. QTc measurements were significantly shorter in patients with positive ATP1A3 variant status ( P P ATP1A3 genotype status was significantly associated with shortened QTc by multivariant regression analysis. Two patients with the ATP1A3‐D801N variant experienced ventricular fibrillation, resulting in death in 1 patient. Rare variants in ATP1A3 were identified in a large cohort of genotype‐negative patients referred for arrhythmia and sudden unexplained death. Conclusions Patients with AHC who carry the ATP1A3‐D801N variant have significantly shorter QTc intervals and an increased likelihood of experiencing bradycardia associated with life‐threatening arrhythmias. ATP1A3 variants may represent an independent cause of sudden unexplained death. Patients with AHC should be evaluated to identify risk of sudden death.

Secondary genomic findings are increasingly being returned to individuals as opportunistic screening results. A secondary finding offers the chance to identify and mitigate disease that may otherwise be unrecognized in an individual. As a form of screening, secondary findings must be considered differently from sequencing results in a diagnostic setting. For these reasons, clinicians should employ an evaluation and long-term management strategy that accounts for both the increased disease risk associated with a secondary finding and the lower positive predictive value of a screening result compared to an indication-based testing result. Here we describe an approach to the clinical evaluation and management of an individual who presents with a secondary finding. This approach enumerates five domains of evaluation—(1) medical history, (2) physical exam, (3) family history, (4) diagnostic phenotypic testing, and (5) variant correlation—through which a clinician can distinguish a molecular finding from a clinicomolecular diagnosis of genomic disease. With this framework, both geneticists and non-geneticist clinicians can optimize their ability to detect and mitigate genomic disease while avoiding the pitfalls of overdiagnosis. Our goal with this approach is to help clinicians translate secondary findings into meaningful recognition, treatment, and prevention of disease.

Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/mL, in plasma diluted 1 to 10) of IFN-α and/or -ω are found in about 10% of patients with critical COVID-19 pneumonia, but not in subjects with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-α and/or -ω (100 pg/mL, in 1/10 dilutions of plasma) in 13.6% of 3,595 patients with critical COVID-19, including 21% of 374 patients80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1,124 deceased patients (aged 20 days-99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-β. We also show, in a sample of 34,159 uninfected subjects from the general population, that auto-Abs neutralizing high concentrations of IFN-α and/or -ω are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4%80 years. Moreover, the proportion of subjects carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals70 years, 2.3% between 70 and 80 years, and 6.3%80 years. By contrast, auto-Abs neutralizing IFN-β do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over-80s, and total fatal COVID-19 cases.

Hypertrophic cardiomyopathy (HCM) has historically been diagnosed phenotypically. Through genetic testing, identification of a molecular diagnosis (MolDx) is increasingly common but the impact on pediatric patients is unknown. This was a retrospective study of next-generation sequencing data for 602 pediatric patients with a clinician-reported history of HCM. Diagnostic yield was stratified by gene and self-reported race/ethnicity. A MolDx of HCM was identified in 242 (40%) individuals. Sarcomeric genes were the highest yielding, but pathogenic and/or likely pathogenic (P/LP) variants in syndromic genes were found in 36% of individuals with a MolDx, often in patients without documented clinical suspicion for a genetic syndrome. Among all MolDx, 73% were in genes with established clinical management recommendations and 2.9% were in genes that conferred eligibility for clinical trial enrollment. Black patients were the least likely to receive a MolDx. In the current era, genetic testing can impact management of HCM, beyond diagnostics or prognostics, through disease-specific guidelines or clinical trial eligibility. Genetic testing frequently can help identify syndromes in patients for whom syndromes may not be suspected. These findings highlight the importance of pursuing broad genetic testing, independent of suspicion based on phenotype. Lower rates of MolDx in Black patients may contribute to health inequities. Further research is needed evaluating the genetics of HCM in underrepresented/underserved populations. Additionally, research related to the impact of genetic testing on clinical management of other diseases is warranted. Supplementary Information The online version contains supplementary material available at 10.1007/s00246-021-02764-1.

Importance Familial hypercholesterolemia (FH) is the most common inherited cardiovascular disease and carries significant morbidity and mortality risks. Genetic testing can identify affected individuals, but some array-based assays screen only a small subset of known pathogenic variants. Objective To identify the number of clinically significant variants associated with FH that would be missed by an array-based, limited-variant screen when compared with next-generation sequencing (NGS)–based comprehensive testing. Design, Setting, and Participants This cross-sectional study compared comprehensive genetic test results for clinically significant variants associated with FH with results for a subset of 24 variants screened by a limited-variant array. Data were deidentified next-generation sequencing results from indication-based or proactive gene panels. Individuals receiving next-generation sequencing–based genetic testing, either for an FH indication between November 2015 and June 2020 or as proactive health screening between February 2016 and June 2020 were included. Ancestry was reported by clinicians who could select from preset options or enter free text on the test requisition form. Main Outcomes and Measures Number of pathogenic or likely pathogenic (P/LP) variants identified. Results This study included 4563 individuals who were referred for FH diagnostic testing and 6482 individuals who received next-generation sequencing of FH-associated genes as part of a proactive genetic test. Among individuals in the indication cohort, the median (interquartile range) age at testing was 49 (32-61) years, 55.4% (2528 of 4563) were female, and 63.6% (2902 of 4563) were self-reported White/Caucasian. In the indication cohort, the positive detection rate would have been 8.4% (382 of 4563) for a limited-variant screen compared with the 27.0% (1230 of 4563) observed with the next-generation sequencing–based comprehensive test. As a result, 68.9% (848 of 1230) of individuals with a P/LP finding in an FH-associated gene would have been missed by the limited screen. The potential for missed findings in the indication cohort varied by ancestry; among individuals with a P/LP finding, 93.7% (59 of 63) of self-reported Black/African American individuals and 84.7% (122 of 144) of Hispanic individuals would have been missed by the limited-variant screen, compared with 33.3% (4 of 12) of Ashkenazi Jewish individuals. In the proactive cohort, the prevalence of clinically significant FH variants was approximately 1:191 per the comprehensive test, and 61.8% (21 of 34) of individuals with an FH-associated P/LP finding would have been missed by a limited-variant screen. Conclusions and Relevance Limited-variant screens may falsely reassure the majority of individuals at risk for FH that they do not carry a disease-causing variant, especially individuals of self-reported Black/African American and Hispanic ancestry.

Data from germline testing in unselected patients with hepatobiliary cancers are limited. Identification of germline predisposition can have important implications on cancer treatment and family counseling. To determine prevalence of pathogenic germline variants (PGV) in patients with hepatobiliary cancer, we undertook a prospective multi-site study of germline sequencing using a >80-gene next-generation sequencing platform among patients with hepatobiliary cancers receiving care at Mayo Clinic Cancer Centers between April 1, 2018 and March 31, 2020. Patients were not selected on the basis of stage, family cancer history, ethnicity, or age. Family cascade testing was offered at no cost. Of 205 patients, the median age was 65 years, 58.5% were male, 81% were White, and 64.4% had cholangiocarcinoma, 21.5% hepatocellular carcinoma, 7.8% gallbladder cancer, and 4.3% carcinoma of ampulla of Vater. PGV were found in 15.6% (n = 32) of patients, including 23 (71%) in moderate and high penetrance cancer susceptibility genes. A total of 75% of patients with a positive result would not have been detected using guidelines for genetic evaluation. Prevalence of PGV was 15.7% in intrahepatic cholangiocarcinoma, 17% in extrahepatic cholangiocarcinoma, 15.9% in hepatocellular cancer, and 33% in carcinoma of ampulla of Vater. On the basis of these genetic findings, 55% were potentially eligible for approved precision therapy and/or clinical treatment trials. Universal multi-gene panel testing in hepatobiliary cancers was associated with detection of heritable mutations in over 15% of patients most of whom would not have been tested using current guidelines. Germline testing should be considered in all patients with hepatobiliary cancers. Prevention Relevance: Universal multi-gene testing in hepatobiliary cancers was associated with heritable mutations in over 15% of patients, most of whom would not have been tested using current guidelines. 55% were potentially eligible for approved precision therapy and/or clinical treatment trials. Germline testing should be considered in all patients with hepatobiliary cancers.

Background: HBOC testing guidelines were established to identify patients with clinically actionable variants and limit economic burden. We report the impact of germline results on health outcome based on clinical decision making and treatment interventions, regardless of guidelines, in a multi-center registry. Methods: 20 community-based and academic sites participated in an IRB approved registry. Patients with breast cancer were tested with an 80-gene panel and clinical information was collected. Results: Data on 912 patients has been analyzed to date. 68% were recently diagnosed and the remaining were diagnosed in the past. 50.5% met NCCN criteria; 49.5% did not. Pathogenic/likely pathogenic (P/LP) germline mutations were found in 8.65% of patients. Of all patients with P/LP findings, 85% had variants in cancer-risk genes with established management recommendations and 80% had germline variants conferring eligibility for clinical trials and precision medicine-based cancer treatments, such as PARP inhibitors. When results were evaluated based on an 11 gene panel of genes most commonly associated with breast cancer, 4.9% (or X) were found to have variants and X percent of these had variants conferring eligibility for clinical trials and precision medicine. X Patients with variants outside of the 11 gene panel had eligibility for clinical trials and precision medicine. There was no significant association between BRCAPRO scores and patients having a P/LP finding, whether in BRCA1/2 alone (p=0.42) or for any cancer gene (p=0.57). For 62% of patients with P/LP germline mutations, clinicians reported results impacted patients’ health outcome; and for 69%, results impacted the health outcome of patients’ relatives. Physician reported impact on patient outcome associated significantly with the presence of P/LP germline findings (p Conclusions: Comprehensive panel testing of breast cancer patients impacts physician assessed patient outcomes and informs changes in surgical treatment strategy, medical therapies and proactive screening. The data suggest that BRCAPRO calculators are poor predictors of germline presence of P/LP findings. Physicians in this study demonstrate the ability to discern the clinically actionable value of P/LP mutations from non-actionable VUS. Multigene panels impact breast cancer patient care by identifying precision medicine treatment interventions and guiding long-term medical management and preventive surveillance for patients and family members. More patients are provided opportunities for precision medicine when a larger panel is used. Table 1. Comprehensive panel clinical management and treatment implications. Germline variants with implications for patient management and treatment. *P/LP variants in these genes confer potential clinical trial eligibility, e.g. NCT02401347.Table 1PatientsVariantsWith breast cancer management guidelines45 (56%)46 (55%)(ATM*, BRCA1*, BRCA2*, CHEK2*, NBN*, NF1, PALB2*, TP53*)With cancer management implications31 (38%)33 (39%)(BARD1*, FH, MITF, MSH6*, MUTYH*, PTCH1, RAD50*, RAD51C*, RAD51D*, RB1, RET, VHL)Evidence of actionability accruing5 (6%)5 (6%)(BLM, DIS3L2, RECQL4)Total8184 Citation Format: Peter Beitsch, Pat Whitworth, Kevin Hughes, Ian Grady, Karen Barbosa, Rakesh Patel, Michael Kinney, Paul Baron, Barry Rosen, Gia Compagnoni, Linda ann Smith, Rache Simmons, Cynara Coomer, Dennis Holmes, Eric Brown, Linsey Gold, Lisa Curcio, Patricia Clark, Tony Ruiz, Heather MacDonald, Sadia Khan, Lee Riley, Sam Lyons, Shan Yang, Mary K Hardwick, Edward D Esplin, Robert L Nussbaum. Comprehensive germline multigene panel testing changes clinical care for patients with breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-28.